Publications

Are you planning to publish a paper involving microscopy ?

You have the possibility to contact the microscopists and/or image analysts in our facility.

The BIOP staff is happy to guide you into following the FAIR principles and provide feedback about your Image Acquisition, Processing, Analysis and Visualization.

Furthermore the BIOP staff can :

  1. Assist in the production of Materials and Methods sections regarding microscopy and image processing.
  2. Advise on data and code accessibility and sharing.
  3. Provide feedback on best practices for data visualization.
  4. Advise on how to share data and code online ( Copyrighting, licensing, uploading ).

Moreover, this provides the BIOP with useful insights how its tools and services have contributed to the scientific literature.

How to acknowledge the BIOP in a publication?

The type of acknowledgement depends on the type of work and collaboration we have undertaken. For publications the rules and recommendations layed out in the EPFL compliance guide apply. 

For contributions to a publication which do not fulfill the criteria above, we recommend the following sentence:  

We would like to thank the EPFL BioImaging & Optics Core Facility and in particular [person(s)] for their assistance in [imaging / image processing].

It has been reported recently [1] that imaging methods are often not properly documented in publications.
In case you have a general question regarding Image acquisition, processing, analysis and visualization, or are unsure what to include into your Materials and Methods section, do not hesitate to drop us a line or pass by. We are happy to:

  1. Assist in the production of Materials and Methods sections regarding microscopy and image processing.
  2. Advise on data and code accessibility and sharing.
  3. Provide feedback on best practices for data visualization.
  4. Advise on how to share data and code online ( Copyrighting, licensing, uploading ).

[1]  Marqués et al.: Science Forum: Imaging methods are vastly underreported in biomedical research, eLife 2020;9:e55133, doi: 10.7554/eLife.55133, Aug 11, 2020.


Latest Publications

Below you will find recent publications by all members of the BioImaging & Optics Platform.

To find all publications, you may head to InfoScience.

2024

Structural and molecular characterization of astrocyte and vasculature connectivity in the mouse hippocampus and cortex

C. Lorin; R. Guiet; N. Chiaruttini; G. Ambrosini; E. Boci et al. 

Glia. 2024. Vol. 72, num. 11, p. 2001 – 2021. DOI : 10.1002/glia.24594.

Supplementary files for Machine learning for histological annotation and quantification of cortical layers

J. Meystre; O. Burri 

2024.

Cellpose training data and scripts from “Inhibition of CERS1 in aging skeletal muscle exacerbates age-related muscle impairments”

M. Wohlwend; O. Burri; J. Auwerx 

2024.

2023

Inhibition of CERS1 in skeletal muscle exacerbates age-related muscle dysfunction

M. Wohlwend; P-P. U. Laurila; L. Goeminne; T. Imamura de Lima; A. Lalou et al. 

eLife. 2023.  p. 35. DOI : 10.7554/eLife.90522.1.

Community-developed checklists for publishing images and image analyses

C. Schmied; M. S. Nelson; S. Avilov; G-J. Bakker; C. Bertocchi et al. 

Nature Methods. 2023. DOI : 10.1038/s41592-023-01987-9.

Compact, high-speed multi-directional selective plane illumination microscopy

R. M. Power; A. Schlaeppi; J. Huisken 

Biomedical Optics Express. 2023. Vol. 14, num. 4, p. 1445 – 1459. DOI : 10.1364/BOE.476217.

Optical imaging of the small intestine immune compartment across scales

A. L. Planchette; C. Schmidt; O. Burri; M. G. de Agueero; A. Radenovic et al. 

Communications Biology. 2023. Vol. 6, num. 1, p. 352. DOI : 10.1038/s42003-023-04642-3.

MoBIE: a Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data

C. Pape; K. Meechan; E. Moreva; M. Schorb; N. Chiaruttini et al. 

Nature Methods. 2023. DOI : 10.1038/s41592-023-01776-4.

Stress granules quantification on fixed and live cells

R. Guiet; X. Xu; F. Stellacci 

2023.

MarrowQuant 2.0: A Digital Pathology Workflow Assisting Bone Marrow Evaluation in Experimental and Clinical Hematology

R. Sarkis; O. Burri; C. Royer-Chardon; F. Schyrr; S. Blum et al. 

Modern Pathology. 2023. Vol. 36, num. 4, p. 100088. DOI : 10.1016/j.modpat.2022.100088.

Sporadic type VI secretion in seventh pandemic Vibrio cholerae

A. Proutière; N. C. Drebes Dorr; L. Bader; S. Stutzmann; L. C. Metzger et al. 

Microbiology. 2023. Vol. 169, num. 5. DOI : 10.1099/mic.0.001329.

2022

In Vivo Retinal Pigment Epithelium Imaging using Transscleral Optical Imaging in Healthy Eyes

L. Kowalczuk; R. Dornier; M. Kunzi; A. Iskandar; Z. Misutkova et al. 

Ophthalmology Science. 2022. Vol. 3, num. 1, p. 100234. DOI : 10.1016/j.xops.2022.100234.

Measuring reporter activity domain in EPI aggregates and Gastruloids.ijm

R. Guiet; O. Burri; M. Girgin; M. Lutolf 

2022.

Microarrayed human bone marrow organoids for modeling blood stem cell dynamics

S. Giger; M. Hofer; M. Miljkovic-Licina; S. Hoehnel; N. Brandenberg et al. 

Apl Bioengineering. 2022. Vol. 6, num. 3, p. 036101. DOI : 10.1063/5.0092860.

Lock-in Raman difference spectroscopy

C. Bonati; V. Fay; R. Dornier; D. Loterie; C. Moser 

Optics Express. 2022. Vol. 30, num. 16, p. 28601 – 28613. DOI : 10.1364/OE.461246.

Sphingolipids control dermal fibroblast heterogeneity

L. Capolupo; I. Khven; A. R. Lederer; L. Mazzeo; G. Glousker et al. 

Science. 2022. Vol. 376, num. 6590, p. 262 – 262. DOI : 10.1126/science.abh1623.

Meeting in the Middle: Towards Successful Multidisciplinary Bioimage Analysis Collaboration

A. Schlaeppi; W. Adams; R. Haase; J. Huisken; R. B. Macdonald et al. 

Frontiers In Bioinformatics. 2022. Vol. 2, p. 889755. DOI : 10.3389/fbinf.2022.889755.

An Open-Source Whole Slide Image Registration Workflow at Cellular Precision Using Fiji, QuPath and Elastix

N. Chiaruttini; O. Burri; P. Haub; R. Guiet; J. Sordet-Dessimoz et al. 

Frontiers In Computer Science. 2022. Vol. 3, p. 780026. DOI : 10.3389/fcomp.2021.780026.

Learning-related congruent and incongruent changes of excitation and inhibition in distinct cortical areas

V. Esmaeili; A. Oryshchuk; R. Asri; K. Tamura; G. Foustoukos et al. 

PLOS Biology. 2022. Vol. 20, num. 5, p. e3001667. DOI : 10.1371/journal.pbio.3001667.

2021

BigDataProcessor2: a free and open-source Fiji plugin for inspection and processing of TB sized image data

C. Tischer; A. Ravindran; S. Reither; N. Chiaruttini; R. Pepperkok et al. 

Bioinformatics. 2021. Vol. 37, num. 18, p. 3079 – 3081. DOI : 10.1093/bioinformatics/btab106.

Conference Posters

You can find our conference posters here in PDF format

ELMI 2017

ELMI 2016